def run(self, debug=False):
print("Running AmiGO:BLAST_Batch")
# temp_output = open(self.outfile + "_temp", "w")
if self.record_index == None:
self.record_index = SeqIO.index(self.infile, "fasta")
print "BLAST infile:%s" % self.infile
# print self.wdir
self.tempfile = self.wdir + "/AmiGO_Record.temp"
go = GOConnector(seq_record=self.record_index, max_query_size=self.batch_size,
e_value_cut_off=self.e_threshold, tempfile=self.tempfile,
debug=self.debug)
go.amigo_batch_mode()
all_seqs = go.all_seqs
all_orfs = dict()
for seq in all_seqs:
key = seq.seq_id
self.results[key] = seq
all_orfs[key] = seq.combined_terms
# print this_seq
# print this_seq.combined_terms
# temp_output.write("%s \t %s\n" % (key, seq.combined_terms))
# temp_output.flush()
# temp_output.close()
self.counter = self.create_counter(all_orfs)
# new_outfile = self.init_output(self.counter,0)
# self.sample = self.update_sample_from_counters(new_outfile, self.counter)
# hasattr
output_csv(self.outfile, self.header, self.counter)
def test_batch_mode(self):
"""
syntax:
http://amigo1.geneontology.org/cgi-bin/amigo/blast.cgi?action=blast&seq=%3ES1%0ATTGAAAAACCTCCGGCTATGCCGGAGGATATTTATTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATATTCTGGAA%3ES2%0AAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCATCTGGTAGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGACGGGACTCGCCGCCGCCCAGCCGGGATTTCCGCTGGCACAATTGAAAACTTTCGTCGACCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATCAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTGTTAGAAGCGCGTGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAA&CMD=Put
http://amigo1.geneontology.org/cgi-bin/amigo/blast.cgi?action=blast&CMD=PUT&expect=0.001&seq=%3ES1%0ATTGTTATCGATCCGGTCGAAAAA
http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi?
action=blast&seq=%3ES1%0ATTGAAAAACCTCCGGCTATGCCGGAGGATATTTATTTC....
%3ES2%0AAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTC...
&CMD=Put
filter
http://amigo1.geneontology.org/cgi-bin/amigo/blast.cgi?action=blast&CMD=Put&maxhits=200&threshold=0.0001&seq=%3ES1%0ATTGTTATCGATCCGGTCGAAAAA
"""
infile = self.data_dir + "AE014075_subTiny10.fasta" # "AE014075_subSmall100.fasta"
record_index = SeqIO.index(infile, "fasta")
go = GOConnector(record_index, 6)
go.create_WebSessions_batches()
self.assertEqual(2, len(go.web_session_list))
go = GOConnector(record_index, 3)
go.create_WebSessions_batches()
self.assertEqual(4, len(go.web_session_list))
go = GOConnector(record_index, 2)
go.create_WebSessions_batches()
self.assertEqual(5, len(go.web_session_list))
self.tempfile = self.data_dir + "AmiGO_Record.temp"
try:
os.remove(self.tempfile)
except OSError:
pass
batch_size = 4
go = GOConnector(record_index, batch_size, tempfile=self.tempfile)
count = go.amigo_batch_mode()
expected = set(['lcl|AE014075.1_gene_1', 'lcl|AE014075.1_gene_2', 'lcl|AE014075.1_gene_3',
'lcl|AE014075.1_gene_4', 'lcl|AE014075.1_gene_5', 'lcl|AE014075.1_gene_6',
'lcl|AE014075.1_gene_7', 'lcl|AE014075.1_gene_8', 'lcl|AE014075.1_gene_9',
'lcl|AE014075.1_gene_10'])
expected_count = math.ceil(10.0 / 4)
self.assertEqual(expected_count, count) # 10/4 round up to 3
for seq in go.all_seqs:
self.assertTrue(seq.seq_id in expected, seq.seq_id)
go = GOConnector(record_index, batch_size, tempfile=self.tempfile)
count = go.amigo_batch_mode() # do nothing
self.assertEqual(0, count)
tempout = open(self.tempfile, "r")
all_lines = tempout.readlines()
tempout.close()
tempout = open(self.tempfile, "w")
for line in all_lines:
tempout.write(line)
if line.startswith("ENDResult"):
break
tempout.close()
go = GOConnector(record_index, batch_size, tempfile=self.tempfile)
resume_count = go.amigo_batch_mode()
self.assertEqual(expected_count - 1, resume_count)
